- recipe bioconductor-amplican
Automated analysis of CRISPR experiments
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/amplican.html
- License:
GPL-3
- Recipe:
`amplican` performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.
- package bioconductor-amplican¶
- versions:
1.24.0-0,1.22.1-0,1.20.0-1,1.20.0-0,1.16.0-2,1.16.0-1,1.16.0-0,1.14.0-0,1.12.0-1,1.24.0-0,1.22.1-0,1.20.0-1,1.20.0-0,1.16.0-2,1.16.0-1,1.16.0-0,1.14.0-0,1.12.0-1,1.12.0-0,1.10.0-0,1.8.0-0,1.6.2-0,1.4.0-0- depends bioconductor-biocgenerics:
>=0.48.0,<0.49.0- depends bioconductor-biocgenerics:
>=0.48.1,<0.49.0a0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0a0- depends bioconductor-biostrings:
>=2.70.0,<2.71.0- depends bioconductor-biostrings:
>=2.70.1,<2.71.0a0- depends bioconductor-genomeinfodb:
>=1.38.0,<1.39.0- depends bioconductor-genomeinfodb:
>=1.38.1,<1.39.0a0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.1,<1.55.0a0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0a0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-s4vectors:
>=0.40.2,<0.41.0a0- depends bioconductor-shortread:
>=1.60.0,<1.61.0- depends bioconductor-shortread:
>=1.60.0,<1.61.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc-ng:
>=12- depends liblapack:
>=3.9.0,<4.0a0- depends libstdcxx-ng:
>=12- depends r-base:
>=4.3,<4.4.0a0- depends r-cluster:
>=2.1.4- depends r-data.table:
>=1.10.4-3- depends r-dplyr:
>=0.7.2- depends r-ggplot2:
>=3.3.4- depends r-ggthemes:
>=3.4.0- depends r-gridextra:
>=2.2.1- depends r-gtable:
>=0.2.0- depends r-knitr:
>=1.16- depends r-matrix:
>=1.2-10- depends r-matrixstats:
>=0.52.2- depends r-rcpp:
- depends r-rmarkdown:
>=1.6- depends r-stringr:
>=1.2.0- depends r-waffle:
>=0.7.0- requirements:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-amplican and update with:: mamba update bioconductor-amplican
To create a new environment, run:
mamba create --name myenvname bioconductor-amplican
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-amplican:<tag> (see `bioconductor-amplican/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-amplican/README.html)
